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Bioinformatics. 2011 Oct 15;27(20):2910-2. doi: 10.1093/bioinformatics/btr481. Epub 2011 Sep 11.

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.

Author information

1
Rega Institute for Medical Research, Clinical and Epidemiological Virology Section, Katholieke Universiteit Leuven, Leuven, Belgium. filip.bielejec@rega.kuleuven.be

Abstract

SUMMARY:

SPREAD is a user-friendly, cross-platform application to analyze and visualize Bayesian phylogeographic reconstructions incorporating spatial-temporal diffusion. The software maps phylogenies annotated with both discrete and continuous spatial information and can export high-dimensional posterior summaries to keyhole markup language (KML) for animation of the spatial diffusion through time in virtual globe software. In addition, SPREAD implements Bayes factor calculation to evaluate the support for hypotheses of historical diffusion among pairs of discrete locations based on Bayesian stochastic search variable selection estimates. SPREAD takes advantage of multicore architectures to process large joint posterior distributions of phylogenies and their spatial diffusion and produces visualizations as compelling and interpretable statistical summaries for the different spatial projections.

AVAILABILITY:

SPREAD is licensed under the GNU Lesser GPL and its source code is freely available as a GitHub repository: https://github.com/phylogeography/SPREAD CONTACT: filip.bielejec@rega.kuleuven.be.

PMID:
21911333
PMCID:
PMC3187652
DOI:
10.1093/bioinformatics/btr481
[Indexed for MEDLINE]
Free PMC Article

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